The Turned Tables
by Texan Rebel
Summary: Post-Fusion: The Federation has put a bounty on Samus' head. This has caught the attention of one bounty hunter that has a particular interest in her. What will happen now? Later HALO cross-over, rated T for some language and violence. UPDATED!
1. Prologue

**The Turned Table**

**Summary: Post-Fusion; the Galactic Federation has put a bounty on Samus' head. This has caught the attention of a bounty hunter who has a particular interest in her. What's going to happen now?**

**A/N: This is my first real attempt at a Metroid fic. Just a heads up, I have not played the games for a while now, so please forgive me if I botch some details. Oh, and another thing; I will later cross-over with HALO. No flames please.**

**A/N: I recently made changes in this chapter and several others to improve story flow.**

**A/N 6/6/13: I am in the process of reworking this story chapter by chapter and eventually completing it. I had to put this on the back burner due to college.**

**Disclaimer: I do not own the rights to Metroid, Nintendo does, or the HALO series, Microsoft and Bungie do.**

**Prologue**

Somewhere in deep space, a small ship drifts silently, camouflaged from radar and visual detection by the latest stealth technology available. The sole occupant slept lightly in the pilots chair while the ships AI manages the ships systems.

The pilot, a freelancer and bounty hunter, is someone that the Federation knows little about other than his contact information and bank routing number, not an easy feat. He catches what may be the last bit of rest for the next few days; his last mission took him deep into the territory of the Space Pirates, to one of their moon sized bases only known by the Federation military and Federation Security Council. It was invulnerable to all but the most clever of attacks and nearly impenetrable; nearly. The designers did not consider an attack from a professional, however. To say the least, there were few survivors; in fact the freelancer almost lost his life in the process of destroying it.

The hired gun always accomplished his missions, and to the letter of his employers requests, making him one of the best and highly sought out in the galaxy by those who heard of him, and the list was short. Allies distrusted him, enemies respected his skill and feared his wrath, only a handful of hunters could do such a feat, Samus Aran being one of them.

One screen on the panel in front of the pilot turned on, disturbing him. As his eyes adjusted to the light, he noticed that he had a message from the Galactic Federation. The address box simply said 'To All Bounty Hunters And Mercenaries', rousing his interest.

The hunter opened the file. It read:

ATTENTION ALL BOUNTY HUNTERS AND MERCENARIES:  
BOUNTY HUNTER SAMUS ARAN HAS BEEN CHARGED WITH TREASON AND CLASS 1 DESTRUCTION OF GALACTIC FEDERATION RESOURCES. SUSPECT IS WANTED DEAD OR ALIVE, COMPENSATION WILL BE GREATER IF RECEIVED ALIVE. ACKNOWLEDGMENT OF TRANSMISSION IS REQUIRED TO CONFIRM ACCEPTANCE OF MISSION.

This surprised the freelancer. What did his fellow hunter do to earn that? He knew the how things worked in the Federations governing body and how individuals were labeled, and this amused the freelancer. He smiled at the prospect of what this was.

Procedure required acknowledgment before any information could be released on the target, including last known location and possible routs of transit. He did have a way to get the information though through illegal means, but that never stopped him before.

It took him only one minute to decide on his next course of action.

**This took me a while. There is plenty more, but it may take a while to get it up due to school. Please review!**


	2. Chapter 1

**A/N: I am uploading this at 0536 hours (that is 5:36 AM for those who don't use the 24-hour system), so please forgive me for any errors. **

**A/N 6/6/13: Working on redoing the whole story with better details, editing, and overall just tidying up the story. Yes, I will finish it, but now I just need to clean it up before I get started on new content.**

**Disclaimer: I own nothing but what I came up with!**

**Chapter I**

Samus frantically maneuvered her ship to avoid laser cannon fire coming from a Federation destroyer. Practically overnight, in fact less than 12 hours after leaving the station, she became Galactic Enemy Number One, all thanks to her crazy ass mission on the Biological Space Labs (BSL) space station above what was at one point planet SR388.

The planet was destroyed by her altering the orbital path of the station so it would crash into the planet. The resulting explosion from the crashing station, the reactors and self-destruct explosives was equal to dozens 100-megaton nuclear warheads detonating simultaneously. The planet was shaken to the core and was quite possibly still breaking apart. Chances of anything surviving were so slim that the odds of survival, even for the X-parasites, were so close to zero that it was not worth the effort of calculating.

Unfortunately the Federation higher-ups and the owners of the station were not particularly thrilled about the destruction of their Metroid breeding program, the space station, a planet, and the X-parasites, which they deemed a highly valuable specimen to study for military applications.

Now Samus was truly alone in her battles. Her list of allies and sanctuaries was growing thin, plus her former employer had turned against her and was hunting her. It wouldn't be long before every other piece of scum that she had a bad encounter with was also on her tail for the rather huge bounty on her head. The closest thing she had to an ally at the moment was the downloaded mind of Adam Malkovich, her old CO from years ago.

"Samus, I detect three more Federation ships closing on our location" Adam announced through the ships speakers.

"What type are they?" she half yelled to the AI, too busy with flying to look for them.

"One carrier and two corvettes; it appears they are holding nothing back to capture you alive Lady."

Samus chuckle at that. "The Federation has sent a fleet after me."

"It appears so. Fighter are being deployed!" Adam warned.

"Oh hell!" She returned bitterly.

Silence filled the cabin once again as the battle out in the vacuum of space raged. The newly arrived Federation ships maneuvered to close off any escape route. Samus saw what they were doing and dodged the incoming fire from the fighters as they chased her. With the odds mounting against her, she wondered how long she could avoid capture.

"Adam, how long until we can jump?" She inquired.

After several seconds he answered. "I calculate that a jump is possible if you can avoid fire for ten three minutes. Loading possible jump points now."

As the ship fought for survival five more Federation ships came out of slip space to join the pursuit. The new arrivals consisted of two destroyers, two more corvettes, and a battleship. It was now nine fully crewed and armed warships plus their fighter squadrons against Samus Aran.

Samus was immediately barraged by fire of every kind from the Federation. Despite all of her battle and flight prowess, she could not avoid all shots. Several blasts took out several of her thrusters, making maneuvering possible but much more difficult to do. Another hit finally eliminated her main engines, effectively crippling her. The fight was over.

In the cockpit, Samus tried franticly to find some way to move, but to no avail. She, Adam, and the creatures she saved from the station, were at the mercy of the Federation.

A transmission soon came in from one of the ships. "Samus Aran," a female voice said, "you are completely surrounded, crippled, and under arrest by order of the Chancellor of the Galactic Federation. Surrender now or we will we fire!"

Samus opened an audio channel to the speaker. "Identify yourself; I want to know who this is."

"This is Fleet Admiral Ferdinand, commander of the Federations 4th Expeditionary Fleet."

The answer was not what she had expected. The 4th fleet was famous for its campaigns against the Space Pirates in their own territory, and succeeding with devastating results. That fleet was hardened and always meant business.

"Adam, what course of action would you consider right now?" she bleakly asked her AI as she slumped into the pilot's seat.

It took a few seconds for him to answer. "Under these circumstances, and our present predicament… surrender is the best option right now. I do not know what will happen after you are arrested however."

Frustration, anger, and defeat was all she felt, but Adam was right. Samus once again opened the channel. "This is Samus Aran… and I surrender" she announced over the radio.

One of the corvettes started to make maneuvers to capture the ship.

**OK, I know this was short and not very interesting at the moment, but I will try to make the others longer and better. Please review, and no flames!**

**A/N: Fixed it up, reviews and opinions would be appreciated.**


	3. Chapter 2

**A/N: I have worked on this for the past few weeks before I felt it was worth posting, so there is quite a bit more to come. After a certain point however, updates will be rather scarce.**

**Disclaimer: Attention any Bungie, Microsoft, and Nintendo employees reading this: I own nothing... Please don't sue me!**

**Chapter II**

As the corvette closed in, a fireball erupted from the ship. Someone or something was attacking the fleet!

Samus activated what few external cameras were left to find the attackers. It was not what she had expected at all; Ridley's space ship and fifteen other Space Pirate warships were closing in.

All Federation communications channels were a mess of officers trying to coordinate and engage the new threat while not hitting or killing their own ships. For whatever reason the Space Pirates showed up, she was reluctantly thankful for their untimely visit.

Two Federation ships were immediately put out of action in the first volley. The remaining vessels used the crippled ones as cover as they started to counterattack. What was to follow was ensured to be a bloodbath for both sides.

While Samus was watching the battle play out in front of her, Adam hacked into the battle network of the Federation to figure out the Federations means of tracking her. It took several minutes, but he soon found what he needed and left undetected.

"Samus," he called to get her attention, "I have done a little 'research' and it appears that the Federation has not only put a tracking device on the ship, but also in your suit. If you have any chance of escaping the Federation you must abandon me and find a different suit to escape in."

"I can't do that; we are drifting in space and my only chance of surviving in space is in the very suit that they are tracking. Either way I am screwed" she stated with defeatin her voice.

A new transmission broke through the insanity on the radio waves, drawing her attention. "Samus, if you want to escape now, you must come with me" a masculine voce said.

Samus answered him, "Who are you and why are you helping me?"

"That's not important now. Are you coming or not?" the man returned.

Adam answered for her. "Of course she'll go. The hatch is on the bottom of the ship however."

"Not a problem. Open the hatch and jump through on my mark."

"Wait," Samus interrupted, "what about my passengers?"

"Bring 'em. You have ten seconds until I dock with you."

Samus quickly got out of her zero suit since it had a tracker and put on a jumpsuit before she grabbed an emergency kit she always had ready and rounded up the creatures that were with her. The hatch opened when the pressure was equal and the creatures went through first.

Before she left, Samus had to ask Adam one last question. "What are you going to do Adam?"

His answer came coolly, like he used to when he commanded her. "End the Federation's legendary Samus Aran. Don't waste this opportunity Lady, you only have one." She understood his reasoning,and jumped down into the ship of her rescuer and sealed the hatch, followed by the sound of decompression and separation.

Samus looked around to gain her bearings and noticed the larger size of the ship. Finding the way to the cockpit, she headed over to it.

When she found the cockpit she saw that it was designed for two pilots but had only one in the left seat. The features of the pilot were blocked by the chair, but noticed that his movements were fluid and precise.

"Feel free to take a seat Ms. Aran." The pilot invited as he continued to manipulate the controls. Samus took the chair next to him on the right side of the cockpit.

She then got a look at the man at the controls. He was well built, dark brown hair in a high-and-tight haircut, and had eyes that were a mix of brown and green. His attire was that of a soldier or mercenary, a black-armored body suit, no visible insignias on it. Unlike most soldiers and other military personnel he had an air of confidence that only highly experienced troops had, but looked no older than her.

"Your AI is going to fake your death, right?" the pilot asked, interrupting her thoughts. She nodded.

He nodded in understanding. He tapped some icons on his panel, causing the lights to dim and redden. Samus looked at him quizzically, not understanding what he was doing. She soon did when she heard the engines hum and she saw the displays show they were cloaked and that the engines were almost ready to jump away from the battle and to freedom.

Samus remembered that she had brought others with her. "I'll make sure my guests are secured before we jump" she said as she left for the back of the ship.

"Be sure to use the dining area, there are plenty of seats there for the critters" He called back.

She quickly finished her task and returned to the cockpit. The pilot was no longer looking at the controls, but the display of the battle raging a long ways away from them.

Samus quickly saw that it was actually on her ship. It was damaged heavily and definitely out of commission. She watched as one of the fighters pushed the vessel towards a corvette. It took several minutes for the fighter to do the task. But it did finish what it started before darting off to fight the Space Pirates.

Not two minutes after the small ship was inside the docking bay did the bay explode, sending parts of the hatch to go flying and causing the ship to vent atmosphere with naval crewmen being sucked out. Adam Malkovich did his part, now it was the hunters turn to do their part.

"May you rest in peace, Adam Malkovich" Samus sadly said.

The pilot gave a quick salute to the fallen AI before he slowly pushed the throttle forward, and they disappeared into slip-space.

**I may take a few days to update, I am not sure yet. If my work load is small enough I may post some more of what I have. Reviews por favor!**


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